Robert Kemp, 27, was taken into custody on Tuesday and released on a $US10,000 ($A10,819) bond the next day.
Kemp is described as a family friend in a news release from Orangeburg County Sheriff Leroy Ravenell.
An arrest warrant said Kemp killed the child “by giving him a bear hug, squeezing the victim so tight that the victim stopped breathing as a result”.
Jaylen Harris died from asphyxiation on June 27, 2013, Orangeburg County Chief Deputy Coroner Sean Fogle said on Wednesday.
Kemp told deputies he was playing with the child when he started to rub his eyes like he was tired, so he put the toddler in his crib on his back with his bottle, according to an incident report.
Kemp said he went to the kitchen to do some chores and realised he hadn’t heard the boy in a while.
He went back into the bedroom and noticed the toddler on his stomach, unconscious with his hands balled into fists, according to the report.
Another person in the home, whose name was blacked out on the report, started CPR, but the boy could not be resuscitated, according to the report.
If convicted, Kemp faces up to five years in prison.
The sheriff’s release didn’t say why it took a year to bring charges, and a spokeswoman for the sheriff said in an email no more information would be released.
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